Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005433.1 Hibiscus syriacus cultivar Beakdansim tig00012455_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 81736
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:8522 original size:14 final size:14
Alignment explanation
Indices: 8503--8529 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8493 TATAAAATCT
8503 TTTTTTATTTTTCA
1 TTTTTTATTTTTCA
8517 TTTTTTATTTTTC
1 TTTTTTATTTTTC
8530 CCTTTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTATTTTTCA
Found at i:10026 original size:35 final size:36
Alignment explanation
Indices: 9948--10049 Score: 197
Period size: 35 Copynumber: 2.9 Consensus size: 36
9938 ACGGTGCTGG
9948 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
9984 ACATTGATACACGAATGTACCAAAGCTGATA-GATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
10019 ACATTGATACACGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
10050 ATACTCAACA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
35 35 0.53
36 31 0.47
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:14459 original size:114 final size:113
Alignment explanation
Indices: 14234--14472 Score: 252
Period size: 114 Copynumber: 2.1 Consensus size: 113
14224 ATTAAGATCA
* * *
14234 AAAGTTTGAATCTTAACATTGTGAATAGAGAAGACTGGATCGGGAGGGTTGTTCCCATAATGAGT
1 AAAGTTTGAATCCTAACATTATGAATAGAGAAGACTGGACCGGGAGGGTTGTTCCCATAATGAGT
* ** *
14299 CATTACAATATCTATCGAATTGAGACATGAAGCTCTTTAATAAAGGTT
66 CATTACAATATCTATCGAATGGAGACATGAAGCTCCCTAATAAAGGTC
* * * *
14347 AGGAGTTTGAATCCTGACATTATGGATAGAGAAGATTGGACCGGGAGGGTT-TTCCTCATAATGA
1 A-AAGTTTGAATCCTAACATTATGAATAGAGAAGACTGGACCGGGAGGGTTGTTCC-CATAATGA
* * * * * *
14411 GTCTTTGCAATATTTATCGAGATGG-GA-A-GCTAGGTTCCCTAATTAAGGTC
64 GTCATTACAATATCTATCGA-ATGGAGACATG--AAGCTCCCTAATAAAGGTC
14461 AAAGTTTGAATC
1 AAAGTTTGAATC
14473 TTGATATTGT
Statistics
Matches: 103, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
112 1 0.01
113 16 0.16
114 83 0.81
115 3 0.03
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (113 bp):
AAAGTTTGAATCCTAACATTATGAATAGAGAAGACTGGACCGGGAGGGTTGTTCCCATAATGAGT
CATTACAATATCTATCGAATGGAGACATGAAGCTCCCTAATAAAGGTC
Found at i:18459 original size:120 final size:117
Alignment explanation
Indices: 18219--18556 Score: 376
Period size: 112 Copynumber: 2.9 Consensus size: 117
18209 TAAAATTGTG
* * *
18219 GGTTAATCTTAAAGTATTTATTTTGATTTTCTAACCTACC---ATTCATATCATCTATTATAAAG
1 GGTTAATCTTAAAGTATTTATTTTAATTTTCTAACCTACCATTATTCAAATCATGTATTATAAAG
* * * * *
18281 ATTTA-TCATGAGACGATTCTCTTTAACTTAGTTTGTTCTATTCATATTTTA
66 ATTTATTCAAGAGACAATTCTCTTTAACTTAGTTTGCTCAATTCACATTTTA
*
18332 -GTTAATCTTAAAGTATTTATTTTAATTTTCTAACCTACCAATTAATTCAGATCATGTATTATAA
1 GGTTAATCTTAAAGTATTTATTTTAATTTTCTAACCTACC-ATT-ATTCAAATCATGTATTATAA
* * *
18396 ATATTTATTGTAAGACAGACAATTCTC-TTAACTTTGTTTGCTCAATTCACA-TTTA
64 AGATTTATT-CAAG--AGACAATTCTCTTTAACTTAGTTTGCTCAATTCACATTTTA
*
18451 GGTTAATCTTAAAGTA--T-TTTTAATTTTCTAACCTATCGATTATTCAAATCATGTATTATAAA
1 GGTTAATCTTAAAGTATTTATTTTAATTTTCTAACCTA-CCATTATTCAAATCATGTATTATAAA
* * * * *
18513 GATTTATT-ATGAGACGATTTTC-TTAACTCAATTTGCTCAATTCA
65 GATTTATTCAAGAGACAATTCTCTTTAACTTAGTTTGCTCAATTCA
18557 TAATATAAAT
Statistics
Matches: 194, Mismatches: 20, Indels: 23
0.82 0.08 0.10
Matches are distributed among these distances:
112 66 0.34
114 2 0.01
116 27 0.14
117 45 0.23
118 3 0.02
119 6 0.03
120 35 0.18
121 10 0.05
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.46
Consensus pattern (117 bp):
GGTTAATCTTAAAGTATTTATTTTAATTTTCTAACCTACCATTATTCAAATCATGTATTATAAAG
ATTTATTCAAGAGACAATTCTCTTTAACTTAGTTTGCTCAATTCACATTTTA
Found at i:19906 original size:23 final size:21
Alignment explanation
Indices: 19864--19927 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 21
19854 TTTTTAACAG
19864 AAAATAAATAATTAAGTAATT
1 AAAATAAATAATTAAGTAATT
19885 AAAATAAAATTAATATAA-TAATT
1 AAAAT-AAA-TAAT-TAAGTAATT
*
19908 -AAATGAAT-ATATAAGTAATT
1 AAAATAAATAAT-TAAGTAATT
19928 CACCCTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 6 0.16
20 6 0.16
21 7 0.18
22 7 0.18
23 9 0.24
24 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
AAAATAAATAATTAAGTAATT
Found at i:20230 original size:18 final size:18
Alignment explanation
Indices: 20203--20237 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20193 GGACTTATGT
*
20203 TTATTTTTTTAAATATTA
1 TTATTGTTTTAAATATTA
*
20221 TTATTGTTTTTAATATT
1 TTATTGTTTTAAATATT
20238 TTCAGCTTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTATTGTTTTAAATATTA
Found at i:22563 original size:6 final size:6
Alignment explanation
Indices: 22552--23422 Score: 1305
Period size: 6 Copynumber: 150.0 Consensus size: 6
22542 ATTTTGTGAT
22552 TATACA TATACA TATACA TATACA TATACA -ATAC- -ATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
22597 TATACA TATACA TATACA TATATAA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATA-CA TATACA TATACA TATACA TATACA
* * *
22646 TATACA TATACA TATACA TACATA TATACA TATACTA CATATCA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATAC-A TATA-CA TATACA
*
22696 TATACA TATACA TAT--A TATACA TATAC- -ATACA TATACA AATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
22740 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
22788 TATAC- -ATACA TATACA TATAC- -ATACA TATACA TATACA TATACC
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
22832 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TACATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA T--ATACA
22882 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TA-ACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
22929 TATACA TATACA TATACA TATACA TATACAA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATAC-A TATACA TATACA TATACA
22978 TATACA TATACA TATACA TATAC- -ATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
23024 TATACA TATACA TATAC- -ATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
23070 TATACA TATACA TATAC- -ATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
23116 TATACA TATACA TATAC- TATACA -ATACA TATACA TATACA TATAC-
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
23161 -ATACA TATAC- -ATACA TATACA TATACA TATACATA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATAC--A TATACA TATACA
23208 TATAC- -AT-CA TATACA TATACA TATACA TATACA TATACA TATAC-
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
23252 -ATACA TATAC- -ATACA TAT-CA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* *
23296 TATAC- TATACA TAT-CA TATACA TACATA TATACA TAT--A TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
23340 TATAC- -ATACA TATACA TATATCA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATA-CA TATACA TATACA TATACA TATACA
* *
23387 TATACA TATACA TATACA TATGCA TATCCA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA
23423 CTGATTCAAT
Statistics
Matches: 800, Mismatches: 19, Indels: 92
0.88 0.02 0.10
Matches are distributed among these distances:
3 1 0.00
4 58 0.07
5 36 0.05
6 667 0.83
7 25 0.03
8 13 0.02
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TATACA
Found at i:24278 original size:17 final size:17
Alignment explanation
Indices: 24237--24282 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
24227 AATTGTCACC
*
24237 CTTAAAAAAATTAAATT
1 CTTAAAAAATTTAAATT
24254 C-TAAAAAATTTAAATT
1 CTTAAAAAATTTAAATT
*
24270 CTTATAAAATTTA
1 CTTAAAAAATTTA
24283 GATATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (17 bp):
CTTAAAAAATTTAAATT
Found at i:31539 original size:26 final size:27
Alignment explanation
Indices: 31499--31554 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
31489 TTCATCTCAA
*
31499 ATTAATTAGAAAAAAAATTGTGTCAAGG
1 ATTAATTAGAAAAAAAA-TGTCTCAAGG
31527 ATTAATTAG-AAAAAAATGTCTCAAGG
1 ATTAATTAGAAAAAAAATGTCTCAAGG
31553 AT
1 AT
31555 GAAAGCGTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 11 0.41
27 7 0.26
28 9 0.33
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (27 bp):
ATTAATTAGAAAAAAAATGTCTCAAGG
Found at i:34427 original size:17 final size:18
Alignment explanation
Indices: 34394--34427 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34384 TACTATTGAT
34394 TTCTAATATACTTTGCAA
1 TTCTAATATACTTTGCAA
*
34412 TTCTAATTTA-TTTGCA
1 TTCTAATATACTTTGCA
34428 TGATTATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (18 bp):
TTCTAATATACTTTGCAA
Found at i:42848 original size:12 final size:12
Alignment explanation
Indices: 42831--42855 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42821 ATAAAATATT
42831 TTCGGGTTTGGG
1 TTCGGGTTTGGG
42843 TTCGGGTTTGGG
1 TTCGGGTTTGGG
42855 T
1 T
42856 ATAATATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.48, T:0.44
Consensus pattern (12 bp):
TTCGGGTTTGGG
Found at i:43915 original size:21 final size:21
Alignment explanation
Indices: 43872--44005 Score: 139
Period size: 21 Copynumber: 6.5 Consensus size: 21
43862 TTTTCCCAAT
* * *
43872 TCGCAATGCGAA-TAAGTAAA
1 TCGCAACGCGAATTGAGAAAA
*
43892 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAATTGAGAAAA
* * *
43913 TCGCAATGCGAA-TAAGTAAA
1 TCGCAACGCGAATTGAGAAAA
*
43933 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAATTGAGAAAA
* * *
43954 TCGCAATGCGAA-TAAGTAAA
1 TCGCAACGCGAATTGAGAAAA
43974 TCGCAACGCGAATTGAGAAAA
1 TCGCAACGCGAATTGAGAAAA
*
43995 TCGCAATGCGA
1 TCGCAACGCGA
44006 TACTGACTAT
Statistics
Matches: 91, Mismatches: 20, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
20 43 0.47
21 48 0.53
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAATTGAGAAAA
Found at i:43917 original size:41 final size:41
Alignment explanation
Indices: 43872--44005 Score: 259
Period size: 41 Copynumber: 3.3 Consensus size: 41
43862 TTTTCCCAAT
43872 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
43913 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
43954 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
43995 TCGCAATGCGA
1 TCGCAATGCGA
44006 TACTGACTAT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:44019 original size:20 final size:20
Alignment explanation
Indices: 43994--44088 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
43984 AATTGAGAAA
*
43994 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
44014 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
44035 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
44055 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
44075 TTCGCAACGCGATA
1 ATCGCAACGCGATA
44089 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:44036 original size:41 final size:41
Alignment explanation
Indices: 43973--44068 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
43963 GAATAAGTAA
* * * *
43973 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAAT-AAAAAATCGCAACGAGATACTGACT
* *
44014 ATCGCAATGCGATAATAAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAATAAAAAATCGCAACGAGATACTGACT
*
44055 TTCGCAACGCGATA
1 ATCGCAACGCGATA
44069 CTGACTTTCG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATAATAAAAAATCGCAACGAGATACTGACT
Found at i:44040 original size:21 final size:20
Alignment explanation
Indices: 43872--44041 Score: 78
Period size: 20 Copynumber: 8.3 Consensus size: 20
43862 TTTTCCCAAT
*
43872 TCGCAATGCG-AATAAGTAAA
1 TCGCAATGCGAAATAA-AAAA
* * **
43892 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAAAT-AAAAAA
*
43913 TCGCAATGCG-AATAAGTAAA
1 TCGCAATGCGAAATAA-AAAA
* * **
43933 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAAAT-AAAAAA
*
43954 TCGCAATGCG-AATAAGTAAA
1 TCGCAATGCGAAATAA-AAAA
* * *
43974 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAAAT-AAAAAA
* * **
43995 TCGCAATGCGATACT-GACTA
1 TCGCAATGCGA-AATAAAAAA
44015 TCGCAATGCGATAATAAAAAA
1 TCGCAATGCGA-AATAAAAAA
44036 TCGCAA
1 TCGCAA
44042 CGAGATACTT
Statistics
Matches: 108, Mismatches: 32, Indels: 19
0.68 0.20 0.12
Matches are distributed among these distances:
20 54 0.50
21 51 0.47
22 3 0.03
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAAATAAAAAA
Found at i:44304 original size:22 final size:22
Alignment explanation
Indices: 44276--44319 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
44266 CACTCTCTCA
44276 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
44298 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
44320 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:44608 original size:20 final size:20
Alignment explanation
Indices: 44583--44620 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44573 TGATTCTCTC
44583 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
44603 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
44621 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:45961 original size:18 final size:18
Alignment explanation
Indices: 45940--45984 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
45930 TCCACTTCGG
*
45940 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
45958 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
45976 GAGCCATCA
1 GAGCCATCA
45985 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:46511 original size:19 final size:20
Alignment explanation
Indices: 46457--46523 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
46447 TAGTTTACTT
* *
46457 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
46477 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
46497 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
46516 TCGCAACG
1 TCGCAACG
46524 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:46531 original size:14 final size:14
Alignment explanation
Indices: 46512--46569 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
46502 ATGCGAAATG
46512 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
46526 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
46542 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
46558 AAAATCGCAACG
1 AAAATCGCAACG
46570 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:46554 original size:32 final size:33
Alignment explanation
Indices: 46496--46586 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
46486 GGAAATGGCT
46496 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
46529 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
46561 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
46587 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:46622 original size:14 final size:14
Alignment explanation
Indices: 46603--46642 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
46593 TTGTGTTTCG
46603 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
46617 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
46631 CGTTGCGATTTT
1 CGTTGCGATTTT
46643 CATTTCGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.07, C:0.15, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:46657 original size:19 final size:19
Alignment explanation
Indices: 46631--46697 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
46621 GCGATTTTGT
**
46631 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
46650 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
46670 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
46689 CGTTGCGAT
1 CGTTGCGAT
46698 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:46677 original size:20 final size:19
Alignment explanation
Indices: 46643--46697 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
46633 TTGCGATTTT
*
46643 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
46662 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
46682 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
46698 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:48699 original size:20 final size:19
Alignment explanation
Indices: 48674--48712 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
48664 TATGTTGAAG
48674 GCAAAACAGACTATCGCAAC
1 GCAAAA-AGACTATCGCAAC
* *
48694 GCAAAATGGCTATCGCAAC
1 GCAAAAAGACTATCGCAAC
48713 AAGAAAATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.41, C:0.28, G:0.18, T:0.13
Consensus pattern (19 bp):
GCAAAAAGACTATCGCAAC
Found at i:48739 original size:19 final size:19
Alignment explanation
Indices: 48715--48782 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
48705 ATCGCAACAA
48715 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
48734 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
48753 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
48767 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
48783 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:48879 original size:19 final size:19
Alignment explanation
Indices: 48803--48876 Score: 112
Period size: 19 Copynumber: 3.8 Consensus size: 19
48793 GCATTGCGAT
* *
48803 TTTCTCGTTGCGATAACCA
1 TTTCGCGTTGCGATAGCCA
48822 TTTTCGCGTTGCGATAGCCA
1 -TTTCGCGTTGCGATAGCCA
*
48842 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGCCA
48861 TTTCGCGTTGCGATAG
1 TTTCGCGTTGCGATAG
48877 TCAAATGAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 34 0.67
20 17 0.33
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.36
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGCCA
Found at i:49960 original size:24 final size:24
Alignment explanation
Indices: 49933--49986 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
49923 GTATTCGAAA
* *
49933 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
49957 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
49981 TTTGAT
1 TTTGAT
49987 GATATTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:50303 original size:14 final size:14
Alignment explanation
Indices: 50284--50320 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
50274 CATCAATTAA
50284 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
50298 ACAAATCACCTTTT
1 ACAAATCAACTTTT
50312 ACAAATCAA
1 ACAAATCAA
50321 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:51743 original size:21 final size:21
Alignment explanation
Indices: 51677--51743 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
51667 GTGAATCGGG
*
51677 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
51697 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
51719 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
51740 CTCT
1 CTCT
51744 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:51762 original size:42 final size:40
Alignment explanation
Indices: 51677--51799 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 40
51667 GTGAATCGGG
* * * *
51677 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAA-GGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
51719 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAA-GGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * *
51761 CTCTTCAAGGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAAGG-TGGGAGGGGACTCTCGA-GGATGATAGG
51800 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
41 6 0.09
42 56 0.82
43 6 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (40 bp):
CTCTTGAAGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:53855 original size:19 final size:19
Alignment explanation
Indices: 53791--53942 Score: 152
Period size: 19 Copynumber: 8.1 Consensus size: 19
53781 TCTTTTGGTT
*
53791 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
53810 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
53830 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
** *
53850 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
53868 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
53883 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
53903 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
53922 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
53941 GA
1 GA
53943 TTTTGGTTTC
Statistics
Matches: 114, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.09
15 2 0.02
18 2 0.02
19 50 0.44
20 48 0.42
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:53971 original size:19 final size:19
Alignment explanation
Indices: 53938--54004 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
53928 AAAATCGCAA
**
53938 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
53957 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
53976 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
53996 TGCGATTTT
1 TGCGATTTT
54005 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:54546 original size:20 final size:20
Alignment explanation
Indices: 54521--54572 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
54511 CGCTATGTAA
54521 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
54541 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
54561 ATCTCGTTGCGA
1 ATCGCGTTGCGA
54573 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:54591 original size:21 final size:21
Alignment explanation
Indices: 54558--54658 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
54548 TGCGAAAGTA
* * *
54558 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
54579 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
54599 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
54621 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
54642 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
54659 CCCAATTTGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:54606 original size:20 final size:20
Alignment explanation
Indices: 54521--54614 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
54511 CGCTATGTAA
*
54521 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
54541 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* ** * *
54561 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTAAGT
* *
54582 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
54602 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
54615 TTTCCCAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 48 0.79
21 13 0.21
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:54633 original size:41 final size:41
Alignment explanation
Indices: 54542--54676 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
54532 AAAGTAAGTA
* * * ** *
54542 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
54582 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
54624 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
*
54665 TTGCGTTGCGAT
1 TCGCGTTGCGAT
54677 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:54647 original size:20 final size:20
Alignment explanation
Indices: 54603--54695 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
54593 ATAGTCAGTA
* **
54603 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
54624 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
54644 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
* *
54665 TTGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
54685 TCGCATTGCGA
1 TCGCATTGCGA
54696 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:54675 original size:21 final size:21
Alignment explanation
Indices: 54603--54678 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
54593 ATAGTCAGTA
*
54603 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* **
54624 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
54644 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
*
54665 TTGCGTTGCGATTT
1 TCGCGTTGCGATTT
54679 ACTTATTCGC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:54677 original size:41 final size:41
Alignment explanation
Indices: 54603--54695 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
54593 ATAGTCAGTA
54603 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
54644 TCGCATTGCGATTTTCCCAATTTGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
54685 TCGCATTGCGA
1 TCGCATTGCGA
54696 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:66817 original size:30 final size:31
Alignment explanation
Indices: 66754--66819 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
66744 ATTTTTTTTT
* * *
66754 TTTTGCAATAACTGAATAAGTTTAATAATTA
1 TTTTACAATAACGGAATAAATTTAATAATTA
66785 TTTTACAATAACGGAATAAATTTAAT-ATTA
1 TTTTACAATAACGGAATAAATTTAATAATTA
66815 TTTTA
1 TTTTA
66820 TAATTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (31 bp):
TTTTACAATAACGGAATAAATTTAATAATTA
Found at i:69114 original size:26 final size:27
Alignment explanation
Indices: 69064--69116 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
69054 TTGTCGCTTG
69064 TTTTAAAGTAATAATATGAATATTTTA
1 TTTTAAAGTAATAATATGAATATTTTA
*
69091 TTTTAAAGTGATATATAT-AA-ATTTTA
1 TTTTAAAGTAATA-ATATGAATATTTTA
69117 GAATCAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 6 0.25
27 14 0.58
28 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (27 bp):
TTTTAAAGTAATAATATGAATATTTTA
Found at i:71943 original size:20 final size:20
Alignment explanation
Indices: 71918--71955 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
71908 GTTTGGTTCA
71918 CGGAATATAAGATTACCAGT
1 CGGAATATAAGATTACCAGT
*
71938 CGGAATGTAAGATTACCA
1 CGGAATATAAGATTACCA
71956 AGGAATAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (20 bp):
CGGAATATAAGATTACCAGT
Done.